To add a bit of information to Asmus' comment:
> What would be a nice first step...would be a serious, coordinated >
effort by leading paleographers to come to an agreement as to
> precisely what kind of information needs to be preserved, and for >
what scripts or paleographic sub-discipline it would be sufficient.

Already in 1990 the Text Encoding Initiative had defined guidelines on
how to mark up texts, particularly for scholarly works. The latest
version, P4, provides recommendations on mark-up for damaged text (see
http://www.tei-c.org/P4X/PH.html#PHDA). For example, it provides tags to
classify the area of damage to a text, the person responsible for
identifying the damage, the degree of damage, etc.

A specific set of guidelines ("EpiDoc") based on TEI was developed by
epigraphers (http://www.ibiblio.org/telliott/epidoc/). A number of
projects with Latin and Greek have implemented these guidelines. One
example is the Vindolanda Tablets Online project
(http://vindolanda.csad.ox.ac.uk/index.shtml), in which uncertain
readings (due to doubtful or partially preserved letters) are rendered
in a different light color (grey). In printed versions, the same letters
are indicated with an underdot. Conceivably style sheets could modify
the uncertain readings as wished.
(Specific information on the text is provided by the "Notes Viewer" and
an image is given, so users can check the image against the text.)

While the TEI and EpiDoc guidelines have been used for Greek, Latin, and
(for TEI) many Western European language materials, they are meant to be
extensible, and could be used for other scripts as well.